Franklin Graham, left, founder of Samaritan's Purse, with his father, Billy Graham, founder of the Billy Graham Evangelistic Association. Franklin Graham says both ministries were targeted by the IRS for audits. (File/AP/Gail Burton)

The ministries founded by Evangelist Billy Graham and his son, Franklin Graham, were audited recently by the Internal Revenue Service, said the son, who believes they were targeted for their conservative stance against gay marriage.

Franklin Graham wrote a letter to President Barack Obama that complained about IRS targeting of conservative groups and alleged that the audits of the Billy Graham Evangelistic Association and Samaritan's Purse were politically motivated.

"I am bringing this to your attention because I believe that someone in the administration was targeting and attempting to intimidate us," Graham wrote to Obama, in a letter dated May 14, 2013.

He said that both ministries were notified in September of audits and visited by IRS agents in October. Both organizations were allowed to keep their tax-exempt status after the audits, he wrote.

In April 2012, the Billy Graham Association had run newspaper advertisements in North Carolina supporting a Marriage Amendment in that state.

Last fall, Samaritan's Purse ran ads nationally urging voters to support candidates "who base their decisions on biblical principles and support the nation of Israel."

Graham said he believed the administration had improperly targeted the ministries in an attempt at intimidation. "This is morally wrong and unethical," Graham wrote. "Indeed, some would call it 'un-American.'"

Graham's allegations come after the IRS admitted focusing attention on Tea Party and Patriot organizations, including some in Alabama.

Billy Graham, America's most famous evangelist, has been known as a friend to presidents since Dwight Eisenhower, including Democrats such as Jimmy Carter and Bill Clinton.

But in 2012 he met with Republican candidate Mitt Romney, and the Billy Graham Association changed language on its web site that had previously described Mormonism as a cult. Graham was widely interpreted as being actively supportive of Romney's campaign.